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https://cran.r-project.org/web/packages/distory/index.html

Software R package for geodesic distance between phylogenetic trees and associated functions.

Proper citation: distory (RRID:SCR_024269) Copy   

•   Source: SciCrunch Registry

https://cran.r-project.org/web/packages/alakazam/index.html

Software R package for high-throughput adaptive immune receptor repertoire sequencing analysis. In particular, immunoglobulin sequence lineage reconstruction, lineage topology analysis, diversity profiling, amino acid property analysis and gene usage.

Proper citation: alakazam (RRID:SCR_024261) Copy   

•   Source: SciCrunch Registry

https://cran.r-project.org/web/packages/ade4/index.html

Software R package for multivariate data analysis. Used for analysis of one-table, two-table, three-table and K-table.

Proper citation: ade4 (RRID:SCR_024259) Copy   

•   Source: SciCrunch Registry

https://bioconductor.org/packages/release/bioc/html/BridgeDbR.html

Software R pacakge provides functions and load identifier mapping databases in R. Uses GitHub, Zenodo, and Figshare if you use this package to download identifier mappings files.

Proper citation: bridgedbr (RRID:SCR_024231) Copy   

•   Source: SciCrunch Registry

https://bioconductor.org/packages/CNEr/

Software R package provides large scale identification and advanced visualization of sets of conserved noncoding elements.

Proper citation: CNEr (RRID:SCR_024233) Copy   

•   Source: SciCrunch Registry

https://bioconductor.org/packages/GenomeInfoDb/

Software R package contains data and functions that define and allow translation between different chromosome sequence naming conventions, including function that attempts to place sequence names in their natural, rather than lexicographic order.

Proper citation: genomeinfodb (RRID:SCR_024235) Copy   

•   Source: SciCrunch Registry

https://bioconductor.org/packages/release/bioc/html/GenomicAlignments.html

Software R package provides efficient containers for storing and manipulating short genomic alignments. This includes read counting, computing the coverage, junction detection, and working with the nucleotide content of the alignments.

Proper citation: genomicalignments (RRID:SCR_024236) Copy   

•   Source: SciCrunch Registry

https://bioconductor.org/packages/release/bioc/html/BiocGenerics.html

Software R package defines many S4 generic functions used in Bioconductor.

Proper citation: BiocGenerics (RRID:SCR_024226) Copy   

•   Source: SciCrunch Registry

https://bioconductor.org/packages/release/bioc/html/biomformat.html

Software R package for interfacing with BIOM format. This package includes basic tools for reading biom-format files, accessing and subsetting data tables from a biom object, limited support for writing biom-object back to biom-format file.

Proper citation: biomformat (RRID:SCR_024228) Copy   

•   Source: SciCrunch Registry

https://bioconductor.org/packages/release/bioc/html/biovizBase.html

Software R package to provide set of utilities, color schemes and conventions for genomic data. Used for various high-level packages for biological data visualization.

Proper citation: biovizBase (RRID:SCR_024229) Copy   

•   Source: SciCrunch Registry

https://bioconductor.org/packages/release/data/annotation/html/GO.db.html

Software R package provides set of annotation maps describing entire Gene Ontology assembled using data from GO.

Proper citation: go.db (RRID:SCR_024241) Copy   

•   Source: SciCrunch Registry

https://bioconductor.org/packages/impute/

Software R package for imputation for microarray data.

Proper citation: impute (RRID:SCR_024243) Copy   

•   Source: SciCrunch Registry

https://bioconductor.org/packages/Mergeomics/

Software R pacakage for multidimensional data integration to identify pathogenic perturbations to biological systems. Used for integrating multidimensional omics disease associations, functional genomics, canonical pathways and gene-gene interaction networks to generate mechanistic hypotheses. Includes Marker set enrichment analysis and Weighted Key Driver Analysis parts.

Proper citation: mergeomics (RRID:SCR_024244) Copy   

•   Source: SciCrunch Registry

https://bioconductor.org/packages/metagenomeSeq/

Software R package to determine features that are differentially abundant between two or more groups of multiple samples. Used to address the effects of both normalization and under-sampling of microbial communities on disease association detection and testing of feature correlations.

Proper citation: metagenomeseq (RRID:SCR_024246) Copy   

•   Source: SciCrunch Registry

https://bioconductor.org/packages/Gviz/

Software R package to perform live annotation queries to Ensembl and UCSC and translates this to e.g. gene/transcript structures in viewports of the grid graphics package.

Proper citation: gviz (RRID:SCR_024239) Copy   

•   Source: SciCrunch Registry

https://cran.r-project.org/package=psychometric

Software R package for measurement theory, meta-analysis, reliability, item analysis, inter-rater reliability, classical utility, and correlation

Proper citation: psychometric (RRID:SCR_024295) Copy   

•   Source: SciCrunch Registry

https://rniftilib.r-forge.r-project.org/

Software R package provides R-interface to the NIfTI reference implementation the niftilib C-library.

Proper citation: rniftilib (RRID:SCR_024296) Copy   

•   Source: SciCrunch Registry

https://cran.r-project.org/package=Rook

Web server for R with documented API to interface between R and the server. The documentation contains the Rook specification and details for building and running Rook applications.

Proper citation: rook (RRID:SCR_024298) Copy   

•   Source: SciCrunch Registry

https://cran.r-project.org/package=RobustRankAggreg

Software R package for aggregating ranked lists, especially lists of genes. RRA method uses a probabilistic model for aggregation that is robust to noise and also facilitates the calculation of significance probabilities for all the elements in the final ranking.

Proper citation: robustrankaggreg (RRID:SCR_024299) Copy   

•   Source: SciCrunch Registry

https://cran.r-project.org/package=rncl

Software R package provides interface to Nexus Class Library which allows parsing of NEXUS, Newick and other phylogenetic tree file formats. Provides elements of file that can be used to build phylogenetic objects such as ape's 'phylo' or phylobase's 'phylo4(d)'.

Proper citation: rncl (RRID:SCR_024290) Copy   

•   Source: SciCrunch Registry